I don't have any test results or extensive knowledge of the internal workings of IV to back up what I am about to say but I think that is hogwash. At some point the NTFS file system will bog down with too many files. Many people say that would be millions of files, while I have heard reports of it being closer to 10,000-40,000 files. In any case 100s of files isn't an issue.
As for IV loading files, having a proper project file that doesn't explicitly specify subfolder paths is the best way to maximize large assembly loading but once again 100s of files aren't enough to really be a problem.
You can read more about this, somewhere on the IV disk is a word doc that explains exactly how IV loads files.